Maxquant Label Free Quantification

[Roddy Fo]

Hi,

I am running peptides identification and quantification on Maxquant version 2.2.0.0.

I found some enriched peptides showed 0 in their intensities in some samples using "match between runs" and  "classic normalization", while some of the same peptides showed high intensity in other samples undergoing the same treatment procedure. 

Can I suspect that the intensity calculation was done by an unknown "filtration" process? Does anybody know how to calculate the intensity from the Maxquant given parameters? Or does anyone know how I can manually check the intensity? 

Best,

Roddy